Cortical connectivity is reorganized by thalamic inputs during postnatal development; however, the precise reorganizational processes and mechanisms are largely unexplored. In the barrel cortex of newborn mice, synaptic activity via thalamocortical (TC) axons is critical for dendritic refinement of layer 4 spiny stellate neurons (barrel cells) into a characteristic dendritic orientation biased toward TC axons at the barrel center. We interrogated the mechanism of dendritic refinement using a combination of in vivo time-lapse imaging and a method to simultaneously label individual barrel cell dendrites and TC axons at the barrel center. The barrel cells reinforced the dendritic orientation toward TC axons by dynamically moving their branches. In N-methyl-D-aspartate receptor (NMDAR)-deficient barrel cells, this dendritic motility was enhanced and the orientation bias was not reinforced. Our data revealed that cortical neurons have "fluctuating" dendrites during the early postnatal period, and NMDAR cell-autonomously regulates these dynamics to establish fine-tuned cortical circuits.